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Salt stress is a worldwide agronomic issue that limits crop yield and quality. Improving salt stress tolerance via genetic modification is the most efficient method to conquer soil salinization problems in crops. Crop miRNAs have been declared to be tightly associated with responding and adapting to salt stress and are advantageous for salt tolerance modification. However, very few studies have validated vital salt tolerance miRNAs and coupled potent target genes in Medicago species, the most economically important forage legume species. In this study, Mtr-miR319a, a miRNA that was identified from the previous next-generation sequencing assay of salt-treated Medicago truncatula, was overexpressed in M. truncatula and Arabidopsis thaliana, inducing the curly leaves and salt stress tolerance phenotypes. Combining the elevated expression level of Mtr-miR319a in the M. truncatula overexpression lines under normal and salt-treatment conditions, the regulatory roles of Mtr-miR319a in leaf development and salt stress adaptation were demonstrated. Several predicted target genes of Mtr-miR319a were also regulated by Mtr-miR319a and were associated with the aforementioned phenotypes in M. truncatula plants, most notably MtTCP4. Our study clarified the functional role of Mtr-miR319a and its target genes in regulating leaf development and defending salt stress, which can help to inform crop breeding efforts for improving salt tolerance via genetic engineering. [ABSTRACT FROM AUTHOR]

Fall dormancy (FD) is an essential trait to overcome winter damage and for alfalfa (Medicago sativa) cultivar selection. The plant regrowth height after autumn clipping is an indirect way to evaluate FD. Transcriptomics, proteomics, and quantitative trait locus mapping have revealed crucial genes correlated with FD; however, these genes cannot predict alfalfa FD very well. Here, we conducted genomic prediction of FD using whole-genome SNP markers based on machine learning-related methods, including support vector machine (SVM) regression, and regularization-related methods, such as Lasso and ridge regression. The results showed that using SVM regression with linear kernel and the top 3000 genome-wide association study (GWAS)-associated markers achieved the highest prediction accuracy for FD of 64.1%. For plant regrowth height, the prediction accuracy was 59.0% using the 3000 GWAS-associated markers and the SVM linear model. This was better than the results using whole-genome markers (25.0%). Therefore, the method we explored for alfalfa FD prediction outperformed the other models, such as Lasso and ElasticNet. The study suggests the feasibility of using machine learning to predict FD with GWAS-associated markers, and the GWAS-associated markers combined with machine learning would benefit FD-related traits as well. Application of the methodology may provide potential targets for FD selection, which would accelerate genetic research and molecular breeding of alfalfa with optimized FD. [ABSTRACT FROM AUTHOR]

As an efficient way of computational target prediction, reverse docking can find not only potential targets but also binding modes for a query ligand. Though the number of available docking tools keeps expanding, there is still not a comprehensive evaluation study which can uncover the advantages and limitations of these strategies in the research field of computational target‐fishing. In this study, we propose a brand‐new evaluation dataset tailor‐made for reverse docking, which is composed of a true positive set (the core set) and two negative sets (the similar decoy set and the dissimilar decoy set). The proposed evaluation dataset can assess the prediction performance of docking tools as various values affected by varying degrees of inter‐target ranking bias. The performance of four classical docking programs (AutoDock, AutoDock Vina, Glide and GOLD) was evaluated utilizing our dataset, and a biased prediction performance was observed regarding binding site properties. The results demonstrated that Glide (SP) and Glide(XP) had the best capacity to find true targets whether there was inter‐target ranking bias or not. [ABSTRACT FROM AUTHOR]

Choline may affect salt tolerance by regulating lipid and glycine betaine (GB) metabolism. This study was conducted to determine whether alteration of lipid profiles and GB metabolism may contribute to choline regulation and genotypic variations in salt tolerance in a halophytic grass, seashore paspalum (Paspalum vaginatum). Plants of Adalayd and Sea Isle 2000 were subjected to salt stress (200‐mM NaCl) with or without foliar application of choline chloride (1 mM). Genotypic variations in salt tolerance and promotive effects of choline application on salt tolerance were associated with both the up‐regulation of lipid metabolism and GB synthesis. The genotypic variations in salt tolerance associated with lipid metabolism were reflected by the differential accumulation of phosphatidylcholine and phosphatidylethanolamine between Adalayd and Sea Isle 2000. Choline‐induced salt tolerance was associated with of the increase in digalactosyl diacylglycerol (DGDG) content including DGDG (36:4 and 36:6) in both cultivars of seashore paspalum and enhanced synthesis of phosphatidylinositol (34:2, 36:5, and 36:2) and phosphatidic acid (34:2, 34:1, and 36:5), as well as increases in the ratio of digalactosyl diacylglycerol: monogalactosyl diacylglycerol (DGDG:MGDG) in salt‐tolerant Sea Isle 2000. Choline regulation of salt tolerance may be due to the alteration in lipid metabolism in this halophytic grass species. Up‐regulation of lipid metabolism and glycine betaine synthesis contributed to choline‐induced salt tolerance in halophytic seashore paspalum and was associated with genotypic variations in salt tolerance. [ABSTRACT FROM AUTHOR]

Plant filamentation temperature-sensitive H (FtsH) proteins are ATP-dependent zinc proteases that play an important role in regulating abiotic stress adaptions. Here we explore their potential role in abiotic stress tolerance in alfalfa, an important legume crop. Genomic analysis revealed seventeen MsFtsH genes in five clusters, which generally featured conserved domains and gene structures. Furthermore, the expression of MsFtsHs was found to be tightly associated with abiotic stresses, including osmotic, salt and oxidative stress. In addition, numerous stress responsive cis -elements, including those related to ABA, auxin, and salicylic acid, were identified in their promoter regions. Moreover, MsFtsH8 overexpression was shown to confer tolerance to salt and oxidative stress which was associated with reduced levels of reactive oxygen species, and enhanced expression and activity of antioxidant enzymes. Our results highlight MsFtsHs as key factors in abiotic stress tolerance, and show their potential usefulness for breeding alfalfa and other crops with improved yield and stress tolerance. • Seventeen MsFtsHs were identified belonging to five groups, which feature conserved domain composition and gene structures. • Stress responsive elements were discovered and 5 MsFtsHs were up-regulated under drought, salt and oxidative stresses. • MsFtsH8 promoted salt and oxidative tolerance in Arabidopsis and alfalfa, providing its role in abiotic stress resistance. [ABSTRACT FROM AUTHOR]

Alfalfa is the most important forage internationally due to its high yield and nutritional value, but its production is severely limited by soil salinization. A better understanding of alfalfa's salt response mechanism is needed to provide guidance for breeding salt tolerant varieties. Lipidomic profiling of the salt-tolerant alfalfa cultivar Medicago sativa cv. Zhongmu-4 was performed after salt treatment. Of the 275 molecular species of lipid identified, 171 had altered levels after salt treatment. The levels of phospholipids, glycolipids, fatty acids, and sphingolipids decreased whereas lysophospholipids and glycerides accumulated in the salt treated plants. Specifically, higher PC/PE and DGDG/MGDG ratios and increased levels of FA 18:3 were observed, suggesting that changes in bilayer membrane structure integrity and fluidity maintenance occur in alfalfa leaves during salt stress. An accumulation of DAG (36:6, 36:5) and TAG (54:8, 54:9, 54:7, 54:6, 52:5, 52:6) was found, consistent with their potential role as storage substrates for membrane regeneration under salt stress. Changes in PI, LPC (16:0, 18:3, 18:2, 18:0), LPE (16:0, 18:2), and Cer (42:1;4 O, 34:1;4 O, 40:1;4 O) suggest these compounds may play a role in signal transduction under salt stress. The levels of PE, DGDG, and TAG were highly correlated (r＞0.8) with changes in salt-related physiological parameters. In addition, the apparent remodeling of lipid profiles was supported by complementary changes in gene expression, including DGD2 , SQD2 , FAD2 , DGK , DGAT , and TAGL , that can be important candidate genes for alfalfa salt tolerance improvement. The detailed description of the changes occurring in lipid profiles and gene expression in alfalfa under salt stress provided by this study implicate lipid remodeling as an important feature of the salt-stress response, and provides a basis for the genetic improvement of alfalfa salt tolerance. • Lipid composition alterations suggest changes in membrane structure integrity and fluidity maintenanc during salt stress. • An accumulation of DAG and TAG indicates their role as storage substrates for membrane regeneration under salt stress. • Genes involved in lipid composition remodeling and storage lipid conversion can be used for salt tolerance improvement. [ABSTRACT FROM AUTHOR]